There is no way to "make IZ stacking more interesting". If the optimal play is to always do it, it's always going to be uninteresting. Now they have an effective diminishing return on industrial buildings and it opens up the door to build more interesting things instead. Using hammers to make more hammers is the least interesting use of hammers there is. It's important to have methods to build up your economy, but there needs to be a point where it makes sense to actually use your economy to build other, non-hammer-related, things instead. The levels of production you got with stacking simply broke the game, I'm not sad to see it go in the slightest.
The overlap bonus only appears with factories/industrialization. So to maximize it, you have to sacrifice the efficiency of your city planning for the first half of the game, where adjacency is a far more important factor (the only one actually).
That's this tension and decision making that made it an interesting puzzle.
You cannot pretend that it "IZ stacking" was the only way to go unless you're ignoring half the game, specially as the first half is one that gives its shape to the game.
This tension between early game and late game doesn't exist anymore.
And I don't think we've played the same game if you think IZ overlap implied only ever building IZs.